Hello,

I am trying to create white matter, grey matter, and CSF masks (along with some other finer segmentations) using Freesurfer, and then use these to find the average BOLD response for all voxels within each mask using AFNI’s 3dmaskave.

So far, I have performed the following steps.

-Talairach-aligned the T1 using @auto_tlrc in AFNI

@auto_tlrc -base TT_N27+tlrc -input  mprage_scan_3+orig

-ran recon-all –notalairach using this T1

recon-all –s 09_07_23_DM –all –notalairach

-created the masks using mri_convert and 3dcalc. For example,

mri_convert -it mgz -ot nii -i aseg.mgz -o aseg.nii

3dcalc -a aseg.nii -expr 'equals(a,4) +equals(a,43) +equals(a,14) +equals(a,15) +equals(a,5) +equals(a,44)' -prefix mask_ventricles_all

I am now attempting ot use 3dmaskave to pull out the average response from talairach aligned trial averages, but I get the error that the input (trial averages – preprocessing and deconvolution done in AFNI) and mask datasets are not the same dimensions.

E.g. 3dmaskave -mask [nameoffile]+orig -quiet s04_trialavg_dt_st_reg_20mmHg20s_10sshifted_al+tlrc > mask_{$roi}_$condition.1D.txt

Any suggestions?

Paula